Pedigree: 1 wildcought female + 90 offspring (5 filtered du to low coverage (< 0.1 Mreads)) Raw data filtration: Clonefilter, ProcessRadtags. Mapping to DTOL
ParentCall with default settings, zlimit=2 (Filtering2 with dataTolerance=)
## 'data.frame': 5574 obs. of 5 variables:
## $ marker_nr : int 5686 6205 5468 5463 6264 6206 6207 6208 6940 6462 ...
## $ male_position: num 0 0 0 0 0 0 0 0 0 0 ...
## $ scaffold : Factor w/ 33 levels "LR999924.1","LR999925.1",..: 5 5 5 5 5 5 5 5 5 5 ...
## $ position : int 2870769 7937849 1897736 1897698 8271669 7937858 7937913 7937917 15276720 10765520 ...
## $ lg : int 1 1 1 1 1 1 1 1 1 1 ...
## [1] "Result from OrderMarker for: DTOL"
## [1] "Number of markers in LG: 5574"
## lg
## 1 337
## 2 262
## 3 229
## 4 253
## 5 243
## 6 253
## 7 160
## 8 240
## 9 208
## 10 162
## 11 182
## 12 267
## 13 176
## 14 242
## 15 201
## 16 175
## 17 209
## 18 361
## 19 174
## 20 163
## 21 132
## 22 94
## 23 196
## 24 110
## 25 90
## 26 135
## 27 100
## 28 79
## 29 41
## 30 33
## 31 67
## scaffold
## LR999924.1 354
## LR999925.1 205
## LR999926.1 248
## LR999927.1 257
## LR999928.1 336
## LR999929.1 176
## LR999930.1 193
## LR999931.1 220
## LR999932.1 203
## LR999933.1 265
## LR999934.1 170
## LR999935.1 242
## LR999936.1 248
## LR999937.1 253
## LR999938.1 206
## LR999939.1 171
## LR999940.1 30
## LR999941.1 190
## LR999942.1 243
## LR999943.1 174
## LR999944.1 143
## LR999945.1 160
## LR999946.1 138
## LR999947.1 94
## LR999948.1 103
## LR999949.1 89
## LR999950.1 155
## LR999951.1 98
## LR999952.1 79
## LR999953.1 62
## LR999954.1 32
## LR999955.1 36
## LR999956.1 1
## [1] "Map length per LG:"
## Group.1 x
## 1 1 84.597
## 2 2 48.917
## 3 3 60.125
## 4 4 83.597
## 5 5 66.783
## 6 6 58.942
## 7 7 64.758
## 8 8 54.505
## 9 9 47.819
## 10 10 46.751
## 11 11 55.641
## 12 12 67.896
## 13 13 50.072
## 14 14 71.216
## 15 15 44.571
## 16 16 70.214
## 17 17 52.414
## 18 18 57.102
## 19 19 73.493
## 20 20 71.441
## 21 21 51.338
## 22 22 26.705
## 23 23 90.331
## 24 24 46.745
## 25 25 52.413
## 26 26 50.116
## 27 27 46.751
## 28 28 43.534
## 29 29 22.482
## 30 30 33.534
## 31 31 59.659
## [1] "Total map length: 1754.462"
library(scales)
##
## Attaching package: 'scales'
## The following object is masked from 'package:viridis':
##
## viridis_pal
#V1=scaffold, V2=position, V3=lg, V4=index, V5=min_int, V6=max_int
map=read.table("mapped_int/order_int_all2.table")
head(map)
## V1 V2 V3 V4 V5 V6
## 1 LR999928.1 7937858 1 1 0 0
## 2 LR999928.1 8009812 1 1 0 0
## 3 LR999928.1 7937849 1 1 0 0
## 4 LR999928.1 7937917 1 1 0 0
## 5 LR999928.1 7938116 1 1 0 0
## 6 LR999928.1 8271669 1 1 1 1
#summary(lm(map$V6~map$V2 + map$V1))
#plot(map[map$V1=="HiC_scaffold_19",]$V2, map[map$V1=="HiC_scaffold_19",]$V6)
#summary(lm(map$V6~map$V2 + map$V1))
NN=unique(map$V3)
MM=1
#unique(map$V4)
cl=rainbow(length(MM))
for(lg in NN) {
print(lg)
#png(paste0("marey", lg, ".png"))
ymax = 0
for (m in MM) {
map_tmp = map[map$V3==lg & map$V4==m,]
ymax = max(ymax, max(map_tmp$V5))
}
index = 1
for (m in MM) {
map_tmp = map[map$V3==lg & map$V4==m,]
if (glm(map_tmp$V2 ~ map_tmp$V5)$coefficients[2] < 0) {
map_tmp$V5 = max(map_tmp$V5) - map_tmp$V5
map_tmp$V6 = max(map_tmp$V6) - map_tmp$V6
}
if (index == 1) {
plot(map_tmp$V2, map_tmp$V5, xlab="Position (Mb)",ylab="Recombination Distance",xaxt="n", main=paste0("LG", lg), col=alpha(cl[index],0.3), pch=20, cex=1.0, ylim=c(0,ymax))
points(map_tmp$V2, map_tmp$V6, col=alpha(cl[index],0.3), pch=20, cex=1.0)
arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length=0.0, col=alpha(cl[index],0.5),lwd=1.5)
}
else {
points(map_tmp$V2, map_tmp$V5, col=alpha(cl[index],0.3), pch=20, cex=1.0)
points(map_tmp$V2, map_tmp$V6, col=alpha(cl[index],0.3), pch=20, cex=1.0)
arrows(map_tmp$V2, map_tmp$V5, map_tmp$V2, map_tmp$V6, length=0.0, col=alpha(cl[index],0.5),lwd=1.5)
}
index = index + 1
}
#dev.off()
}
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